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XCMS Results Table

I am wondering if anyone knows what determines which molecular features get into the XCMS online results table. There seems to be some sort of cut off, but it is not clear what it is. Does the table represent all features detected in the entire data set or only a subset?

Re: XCMS Results Table

Reply #1 –
Quinnr,

All features are seen in the results table which pass the minfrac cut off. Minfrac is a robustness filter to make sure that the feature is seen reproducibly across the class group. If minfrac is set at 50% (ie 0.5) then we have to see feature X in at least 50% of the samples for class 1. For example, if we have 3 classes WT, MUT-1, MUT-2. Each class has 6 samples each. A feature will appear in the report if the feature is seen/detected in at least 3 samples (50%) of any one class. So, we could see feature X in the samples of WT 3 times but not see them in the MUT-1 samples or the MUT-2 samples and the feature X would still appear in the report. However, if feature Y was seen 2 times in the samples of class WT, 1 sample of MUT-1 and in 2 samples of MUT-2 then it would not pass the minfrac filter.

Hope this helps and sorry for the delay in response.

Paul
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page

Re: XCMS Results Table

Reply #2 –
Quote from: "hpbenton"
Quinnr,

All features are seen in the results table which pass the minfrac cut off. Minfrac is a robustness filter to make sure that the feature is seen reproducibly across the class group. If minfrac is set at 50% (ie 0.5) then we have to see feature X in at least 50% of the samples for class 1. For example, if we have 3 classes WT, MUT-1, MUT-2. Each class has 6 samples each. A feature will appear in the report if the feature is seen/detected in at least 3 samples (50%) of any one class. So, we could see feature X in the samples of WT 3 times but not see them in the MUT-1 samples or the MUT-2 samples and the feature X would still appear in the report. However, if feature Y was seen 2 times in the samples of class WT, 1 sample of MUT-1 and in 2 samples of MUT-2 then it would not pass the minfrac filter.

Hope this helps and sorry for the delay in response.

Paul

Hi

I am new to GCMS and XCMS. Why there is different features with different m/z for the same retention time in results table?
I am looking forward to seeing your kind reply.

Cheers
 

Re: XCMS Results Table

Reply #3 –
Hi hpbenton,

Your explication is interesting for me. Could you tell me please how we should arrange our data before applying xcms? Should we create 3 files for example, for theses 3 classes or just put all the 18 samples in one single file?

Up to now, I always create files equal to the number of my classes, but my minfrac is 0.05. I think it's too small, isn't it?

Thank you in advance